Primer Show accepts a DNA sequence along with a set of primer sequences and returns a textual map showing the annealing positions of the primers. The translation of the DNA sequence can be shown in the reading frames you specify. You can also choose the number of bases per line of the map, and whether to show the DNA in its single-stranded or double-stranded form. The primer sequences you enter can contain "wild card" bases, a feature that allows Primer Show to handle degenerate primers. Use this program to produce a useful reference figure, particularly when you have designed a large number of primers for a particular template.
Paste the raw or FASTA sequence into the text area below. >mRNA /gene="fem-2" (exons in uppercase) gaacgcgaatgcctctctctctttcgatgggtatgccaattgtccacattcactcgtgttgcctcctctttgccaacacgcaagacaccagaaacgcgtcaaccaaagagaaaaagacgccgacaacgggcagcactcgcgagagacaaaggttatcgcgttgtgttattatacattcgcatccgggtcaactttagtccgttgaacatgcttcttgaaaacctagttctcttaaaataacgttttagaagttttggtcttcagATGTCTGATTCGCTAAATCATCCATCGAGTTCTACGGTGCATGCAGATGATGGATTCGAGCCACCAACATCTCCGGAAGACAACAACAAAAAACCGTCTTTAGAACAAATTAAACAGGAAAGAGAAGCGTTGTTTACGgttagttacctattagctgcaagttttgaaaaagcggaatctgtaaaaagcggaatctgtaaaaaaaacatctaaggaataattctgaaaagaaaaagtttctaaatgttaatcggaatccaatttttatgaaattatttaaaaaaaaactaaaattagtttctaaaaaatttttctaaagtaattggaccatgtgaaggtacacccacttgttccaatatgccatatctaactgtaaaataatttgattctcatgagaatatttttcagGATCTATTCGCAGATCGTCGACGAAGCGCTCGTTCTGTGATTGAAGAAGCTTTCCAAAACGAACTCATGAGTGCTGAACCAGTCCAGCCAAACGTGCCGAATCCACATTgtgagttggaaatttttatttgataaccaagagaaaaaaagttctacctttttttcaaaaacctttccaaaaatgattccatctgatataggattaagaaaaatattttccgaaatctctgcttttcagCGATTCCCATTCGTTTCCGTCATCAACCAGTTGCTGGACCTGCTCATGATGTTTTCGGAGACGCGGTGCATTCAATTTTTCAAAAAATAATGTCCAGgtatacactatttttgcatatttttcttgccaaatttggtcaaaaaccgtagtacaacccaaaaagtttcttcatttcagAGGAGTGAACGCGGATTATAGTCATTGGATGTCATATTGGATCGCGTTGGGAATCGACAAAAAAACACAAATGAACTATCATATGAAACCGTTTTGCAAAGATACTTATGCAACTGAAGGCTCCTTAGgtaggttagtcttttctaggcacagaagagtgagaaaattctaaatttctgagcagtctgctttttgttttccttgagtttttacttaaagctcttaaaagaaatctaggcgtgaagttcgagccttgtaccataccacaacagcattccaaatgttacagAAGCGAAACAAACATTTACTGATAAAATCAGGTCAGCTGTTGAGGAAATTATCTGGAAGTCCGCTGAATATTGTGATATTCTTAGCGAGAAGTGGACAGGAATTCATGTGTCGGCCGACCAACTGAAAGGTCAAAGAAATAAGCAAGAAGATCGTTTTGTGGCTTATCCAAATGGACAATACATGAATCGTGGACAGgttagtgcgaatcggggactcaagatttactgaaatagtgaagagaaaacaaaagaaaactatattttcaaaaaaaatgagaactctaataaacagaatgaaaaacattcaaagctacagtagtatttccagctggagtttccagagccaaaaaaatgcgagtattactgtagttttgaaattggtttctcactttacgtacgattttttgatttttttttcagactcttcatatgaaaaaaaatcatgttttctcctttacaagatttttttgatctcaaaacatttccagAGTGACATTTCACTTCTTGCGGTGTTCGATGGGCATGGCGGACACGAGTGCTCTCAATATGCAGCTGCTCATTTCTGGGAAGCATGGTCCGATGCTCAACATCATCATTCACAAGATATGAAACTTGACGAACTCCTAGAAAAGGCTCTAGAAACATTGGACGAAAGAATGACAGTCAGAAGTGTTCGAGAATCTTGGAAAGGTGGAACCACTGCTGTCTGCTGTGCTGTTGATTTGAACACTAATCAAATCGCATTTGCCTGGCTTGGAGATTCACCAGGgtaatcaatttttttttagtttttggaactttacgtcccgaaaaattattcctttatcacctaattcctacagtaacccaagctccgaattaaataaagttaaagcgtggtatacacataaaaataagaaaaaattgttcatgaaatccatttttccagTTACATCATGTCAAACTTGGAGTTCCGCAAATTCACTACTGAACACTCCCCGTCTGACCCGGAGGAATGTCGACGAGTCGAAGAAGTCGGTGGCCAGATTTTTGTGATCGGTGGTGAGCTCCGTGTGAATGGAGTACTCAACCTGACGCGAGCACTAGGAGACGTACCTGGAAGACCAATGATATCCAACAAACCTGATACCTTACTGAAGACGATCGAACCTGCGGATTATCTTGTTTTGTTGGCCTGTGACGGGATTTCTGACGTCTTCAACACTAGTGATTTGTACAATTTGGTTCAGGCTTTTGTCAATGAATATGACGTAGAAGgtatcaaactgatcgtttttcacatcacaaaattcttgaattttccagATTATCACGAACTTGCACGCTACATTTGCAATCAAGCAGTTTCAGCTGGAAGTGCTGACAATGTGACAGTAGTTATAGGTTTCCTCCGTCCACCAGAAGACGTTTGGCGTGTAATGAAAACAGACTCGGATGATGAAGAGAGCGAGCTCGAGGAAGAAGATGACAATGAATAGtttattgcaagttttccaaaacttttccaatttccctgggtattgattagcatccatatcttacggcgattatatcaattgtaacattatttctgtttctccccccacctctcaaattttcaaatgaccctttttcttttcgtctacctgtatcgttttccattcatctccccccctccactgtggtatatcattttgtcattagaaagtattattttgattttcattggcagtagaagacaacaggatacagaagaggttttcacag
Enter the patterns in the 5' to 3' direction. An example pattern is: /ac[gt]agcct/ (My pattern's name). The two slashes mark the boundary of the pattern and the round brackets surround the name of the pattern. The square brackets surround possible bases at a degenerate site. You can enter multiple patterns separated by commas. Primer Show automatically constructs a reverse-complement version of each primer sequence so that matches on the reverse strand can be shown. Incorrect entry of the patterns may produce errors.
Enter the genetic code expressions. The default set of expressions describes the standard genetic code. Slashes mark the boundary of the pattern to match, while the equal sign and letter specify the amino acid described by the pattern. Within the pattern square brackets surround possible bases present at a single position. The vertical bar separates two distinct patterns that represent the same amino acid. Each expression is followed by a comma, except for the last expression. /gc[agtcn]/=A, /tg[ct]/=C, /ga[tc]/=D, /ga[ag]/=E, /tt[tc]/=F, /gg[agctn]/=G, /ca[tc]/=H, /at[atc]/=I, /aa[ag]/=K, /ct[agtcn]|tt[ag]/=L, /atg/=M, /aa[tc]/=N, /cc[atgcn]/=P, /ca[ag]/=Q, /cg[agctn]|ag[ag]/=R, /tc[agctn]|ag[ct]/=S, /ac[agctn]/=T, /gt[agctn]/=V, /tgg/=W, /ta[tc]/=Y, /ta[ga]|tga/=*
